diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bnw.scm | 90 |
1 files changed, 52 insertions, 38 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm index 2c34256..7b6662c 100644 --- a/gn/packages/bnw.scm +++ b/gn/packages/bnw.scm @@ -2,12 +2,12 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix git-download) - #:use-module (guix build-system trivial) - #:use-module (gnu packages bash) + #:use-module (guix build-system gnu) #:use-module (gn packages graphviz) #:use-module (gn packages javascript) #:use-module (gn packages maths) #:use-module (gnu packages python) + #:use-module (gnu packages statistics) #:use-module (gn packages web)) (define-public bnw @@ -25,44 +25,45 @@ (sha256 (base32 "10qwykp2zcyxih6a52icvy30ps69qk4v3jgirmdpw1l15zi4p2wq")))) - (build-system trivial-build-system) + (build-system gnu-build-system) (arguments - `(#:modules ((guix build utils)) - #:builder - (begin - (use-modules (guix build utils)) - (let* ((out (assoc-ref %outputs "out")) - (source (assoc-ref %build-inputs "source")) - (bash (assoc-ref %build-inputs "bash")) - (graphviz (assoc-ref %build-inputs "graphviz")) - (octave (assoc-ref %build-inputs "octave")) - (python (assoc-ref %build-inputs "python")) - (jquery (assoc-ref %build-inputs "jquery")) - (awesome (assoc-ref %build-inputs "awesome")) - (cyto (assoc-ref %build-inputs "cytoscape")) - (cyto2 (assoc-ref %build-inputs "cytoscape-2")) - (cs-dagre (assoc-ref %build-inputs "cyto-dagre")) - (d3js (assoc-ref %build-inputs "d3js")) - (d3js-multi (assoc-ref %build-inputs "d3js-multi")) - (dagre (assoc-ref %build-inputs "dagre")) - (lodash (assoc-ref %build-inputs "lodash")) - (canvas-toblob (assoc-ref %build-inputs "canvas-toblob")) - (filesaver (assoc-ref %build-inputs "filesaver")) - (panzoom (assoc-ref %build-inputs "panzoom")) - (js-path "/share/genenetwork2/javascript/")) - (copy-recursively source out) - (for-each (lambda (file) - (patch-shebang file - (list (string-append bash "/bin") - (string-append octave "/bin") - (string-append python "/bin")))) - (find-files out ".*")) - (with-directory-excursion out + `(#:tests? #f ; no test suite + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'patch-source-shebangs 'patch--more-shebangs + (lambda* (#:key inputs #:allow-other-keys) + (let* ((bash (assoc-ref inputs "bash")) + (graphviz (assoc-ref inputs "graphviz")) + (octave (assoc-ref inputs "octave")) + (python (assoc-ref inputs "python")) + (rmath (assoc-ref inputs "rmath")) + (jquery (assoc-ref inputs "jquery")) + (awesome (assoc-ref inputs "awesome")) + (cyto (assoc-ref inputs "cytoscape")) + (cyto2 (assoc-ref inputs "cytoscape-2")) + (cs-dagre (assoc-ref inputs "cyto-dagre")) + (d3js (assoc-ref inputs "d3js")) + (d3js-multi (assoc-ref inputs "d3js-multi")) + (dagre (assoc-ref inputs "dagre")) + (lodash (assoc-ref inputs "lodash")) + (canvas-toblob (assoc-ref inputs "canvas-toblob")) + (filesaver (assoc-ref inputs "filesaver")) + (panzoom (assoc-ref inputs "panzoom")) + (js-path "/share/genenetwork2/javascript/")) + (for-each (lambda (file) + (patch-shebang file + (list (string-append bash "/bin") + (string-append octave "/bin") + (string-append python "/bin")))) + (find-files "." ".*")) (substitute* (append '("home.php") (find-files "sourcecodes" ".php") (find-files "sourcecodes/run_scripts" ".*")) (("/usr/bin/dot") (string-append graphviz "/bin/dot"))) + (substitute* "sourcecodes/build.sh" + (("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so"))) (substitute* "sourcecodes/layout_cyto.php" (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js") (string-append cyto js-path "cytoscape/cytoscape.min.js")) @@ -91,13 +92,26 @@ (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js") (string-append canvas-toblob js-path "canvas-toBlob/canvas-toBlob.js")) (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js") - (string-append filesaver js-path "filesaver/filesaver.js")))))))) - (native-inputs `(("source" ,source))) + (string-append filesaver js-path "filesaver/filesaver.js")))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (delete-file "sourcecodes/localscore/libRmath.so") + (copy-recursively "." out)) + #t)) + (replace 'build + (lambda _ + (with-directory-excursion "sourcecodes" + (substitute* "build.sh" + (("./localscore") "localscore")) + (chmod "k-best/src/buildk_poster.sh" #o755) + (invoke "sh" "build.sh"))))))) (inputs - `(("bash" ,bash-minimal) - ("graphviz" ,graphviz-2.26) + `(("graphviz" ,graphviz-2.26) ("octave" ,octave-3.4.3) ("python" ,python-2) + ("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version? ("jquery" ,web-jquery) ("awesome" ,web-font-awesome) ("cytoscape" ,javascript-cytoscape) |